5-year survival for head and neck squamous cell carcinoma (HNSCC) is only 50%, and very variable. Survival cannot be accurately predicted through standard histopathology. Recently, a subset of approximately 30% of the HNSCC has been shown to contain HPV. In comparison to HPV-negative tumors, HPV-positive HNSCCs are more likely to be located within the oral cavity/pharynx, poorly differentiated, and diagnosed at a late stage. The HPV DNA (overwhelmingly genotype 16, a high-risk type also found in cervical cancer) in these tumors is present at high copy numbers, is frequently integrated, and is often transcriptionally active (e.g., expression of the viral oncoproteins E6 and E7). Surprisingly, despite being more advanced at diagnosis, HPV-positive HNSCC is associated with better response to therapy and longer survival than HPV-negative tumors. Thus, HPV-positive and-negative HNSCC appear to be clinically and biologically distinct. The differences in in clinical and biologic characteristics that distinguish HPV-positive and-negative HNSCC are likely to be explained by differences in RNA expression. Our proposed study will be the first to compare and contrast gene expression in HPV-positive and-negative HNSCC. Specifically, under this application frozen tumor samples from 112 HNSCC patients undergoing surgery at Montefiore Medical Center, New York, will be assessed for presence of HPV DNA on a type-specific basis using a well established sensitive PCR assay, and the expression of the viral oncoproteins E6 and E7 using RT-PCR. This project exploits ongoing (currently funded research) to characterize gene expression patterns in HNSCC tumors using a novel high-throughput microarray method with 28,000 cDNA clones developed and previously validated by our team. Detailed[unreadable] data on clinical characteristics are being collected prospectively following an approved study design and standardized clinical review criteria. This data will be used to study: (i) the association of HPV with characteristics of HNSCC; (ii) differences in gene expression profiles between HPV-positive and-negative HNSCC; and (iii) the relation of these gene expression profiles with disease free and overall survival.